Variant report

Variant	rs9949
Chromosome Location	chr8:8994512-8994513
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr8:8991597-8999830	HUVEC	blood vessel:	n/a	n/a
2	POLR2A	chr8:8991535-8995004	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr8:8994458-8994620	GM12878	blood:	n/a	n/a
4	POLR2A	chr8:8992645-8997055	K562	blood:	n/a	n/a
5	POLR2A	chr8:8994402-8994716	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:8993866..8996087-chr8:9007347..9008899,2	K562	blood:
2	chr8:8982946..8984687-chr8:8992540..8994989,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000254340	TF binding region
ENSG00000173281	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs12785	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs189798	0.87[EUR][1000 genomes]
rs330903	0.80[EUR][1000 genomes]
rs330904	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs330905	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs330908	0.91[CEU][hapmap];0.86[CHB][hapmap];0.89[JPT][hapmap];0.88[TSI][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs330909	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs330910	1.00[CEU][hapmap];0.94[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs330911	0.86[CEU][hapmap];0.86[CHB][hapmap];0.82[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs330912	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs330913	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs330914	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs330915	0.91[CEU][hapmap];0.86[CHB][hapmap];0.89[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs330916	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs330917	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs330918	0.81[EUR][1000 genomes]
rs330919	0.85[CHB][hapmap];0.82[JPT][hapmap];0.88[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs330920	0.87[CEU][hapmap];0.81[CHB][hapmap];0.89[JPT][hapmap];0.88[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs330921	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs330922	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs330923	0.95[CEU][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs330924	0.84[AMR][1000 genomes]
rs330927	0.86[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917117	chr8:8621658-9313799	Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv1022468	chr8:8857853-9209167	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv539460	chr8:8857853-9209167	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv817373	chr8:8857854-9361049	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	nsv1022328	chr8:8954003-9061281	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	nsv610206	chr8:8961017-9162048	Genic enhancers Strong transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
7	nsv1026279	chr8:8982622-9030279	Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	n/a
8	nsv949434	chr8:8993551-9318404	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9949	PPP1R3B	cis	Lymphoblastoid	GTEx
rs9949	PPP1R3B	cis	multi-tissue	Pritchard

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:8987800-8997400	Weak transcription	Spleen	Spleen
2	chr8:8989200-8997400	Weak transcription	Gastric	stomach
3	chr8:8989600-8996800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr8:8990200-8995200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr8:8990400-8994800	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr8:8990400-8997600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr8:8992400-8994800	Enhancers	Stomach Mucosa	stomach
8	chr8:8992600-9000000	Weak transcription	Hela-S3	cervix
9	chr8:8992800-8994600	Enhancers	iPS-15b Cell Line	embryonic stem cell
10	chr8:8992800-8995000	Weak transcription	Lung	lung
11	chr8:8993000-8994600	Enhancers	iPS-18 Cell Line	embryonic stem cell
12	chr8:8993200-8994800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr8:8993200-8995400	Enhancers	Right Ventricle	heart
14	chr8:8993400-8994800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr8:8993400-8994800	Weak transcription	Placenta	Placenta
16	chr8:8993400-8995000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr8:8993400-8995200	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr8:8993400-8996200	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr8:8993400-8997200	Weak transcription	Esophagus	oesophagus
20	chr8:8993400-8997400	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr8:8993400-8997800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr8:8993600-8994600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
23	chr8:8993600-8995000	Enhancers	Liver	Liver
24	chr8:8993600-8996400	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr8:8993600-9005400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr8:8993800-8994600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
27	chr8:8993800-8994800	Enhancers	Fetal Intestine Small	intestine
28	chr8:8993800-8995800	Enhancers	Primary T helper cells fromperipheralblood	blood
29	chr8:8993800-8997400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr8:8993800-8997600	Weak transcription	Primary T cells fromperipheralblood	blood
31	chr8:8993800-8997600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr8:8993800-8997600	Weak transcription	HMEC	breast
33	chr8:8993800-8998400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr8:8993800-8998600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr8:8993800-9007400	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr8:8994000-8994800	Enhancers	Psoas Muscle	Psoas
37	chr8:8994000-8996200	Weak transcription	Primary T cells from cord blood	blood
38	chr8:8994000-8997200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr8:8994000-8997600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr8:8994000-8997600	Weak transcription	Brain Substantia Nigra	brain
41	chr8:8994000-8997600	Weak transcription	Thymus	Thymus
42	chr8:8994000-8997800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr8:8994000-8997800	Weak transcription	Brain Hippocampus Middle	brain
44	chr8:8994200-8994600	Genic enhancers	HUES6 Cell Line	embryonic stem cell
45	chr8:8994200-8994600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr8:8994200-8994600	Enhancers	Breast Myoepithelial Primary Cells	Breast
47	chr8:8994200-8994600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr8:8994200-8994600	Flanking Active TSS	GM12878-XiMat	blood
49	chr8:8994200-8994800	Enhancers	Fetal Intestine Large	intestine
50	chr8:8994200-8994800	Weak transcription	Fetal Muscle Trunk	muscle

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